keyword
MENU ▼
Read by QxMD icon Read
search

Bacterial whole genome sequencing

keyword
https://www.readbyqxmd.com/read/27914076/reconstructing-the-ancestral-relationships-between-bacterial-pathogen-genomes
#1
Caitlin Collins, Xavier Didelot
Following recent developments in DNA sequencing technology, it is now possible to sequence hundreds of whole genomes from bacterial isolates at relatively low cost. Analyzing this growing wealth of genomic data in terms of ancestral relationships can reveal many interesting aspects of the evolution, ecology, and epidemiology of bacterial pathogens. However, reconstructing the ancestry of a sample of bacteria remains challenging, especially for the majority of species where recombination is frequent. Here, we review and describe the computational techniques currently available to infer ancestral relationships, including phylogenetic methods that either ignore or account for the effect of recombination, as well as model-based and model-free phylogeny-independent approaches...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27912842/the-rapid-spread-of-carbapenem-resistant-enterobacteriaceae
#2
REVIEW
Robert F Potter, Alaric W D'Souza, Gautam Dantas
Carbapenems, our one-time silver bullet for multidrug resistant bacterial infections, are now threatened by widespread dissemination of carbapenem-resistant Enterobacteriaceae (CRE). Successful expansion of Enterobacteriaceae clonal groups and frequent horizontal gene transfer of carbapenemase expressing plasmids are causing increasing carbapenem resistance. Recent advances in genetic and phenotypic detection facilitate global surveillance of CRE diversity and prevalence. In particular, whole genome sequencing enabled efficient tracking, annotation, and study of genetic elements colocalized with carbapenemase genes on chromosomes and on plasmids...
November 2016: Drug Resistance Updates: Reviews and Commentaries in Antimicrobial and Anticancer Chemotherapy
https://www.readbyqxmd.com/read/27912729/genomic-insights-from-whole-genome-sequencing-of-four-clonal-outbreak-campylobacter-jejuni-assessed-within-the-global-c-jejuni-population
#3
Clifford G Clark, Chrystal Berry, Matthew Walker, Aaron Petkau, Dillon O R Barker, Cai Guan, Aleisha Reimer, Eduardo N Taboada
BACKGROUND: Whole genome sequencing (WGS) is useful for determining clusters of human cases, investigating outbreaks, and defining the population genetics of bacteria. It also provides information about other aspects of bacterial biology, including classical typing results, virulence, and adaptive strategies of the organism. Cell culture invasion and protein expression patterns of four related multilocus sequence type 21 (ST21) C. jejuni isolates from a significant Canadian water-borne outbreak were previously associated with the presence of a CJIE1 prophage...
December 3, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27910897/genomic-variations-leading-to-alterations-in-cell-morphology-of-campylobacter-spp
#4
Diane Esson, Alison E Mather, Eoin Scanlan, Srishti Gupta, Stefan P W de Vries, David Bailey, Simon R Harris, Trevelyan J McKinley, Guillaume Méric, Sophia K Berry, Pietro Mastroeni, Samuel K Sheppard, Graham Christie, Nicholas R Thomson, Julian Parkhill, Duncan J Maskell, Andrew J Grant
Campylobacter jejuni, the most common cause of bacterial diarrhoeal disease, is normally helical. However, it can also adopt straight rod, elongated helical and coccoid forms. Studying how helical morphology is generated, and how it switches between its different forms, is an important objective for understanding this pathogen. Here, we aimed to determine the genetic factors involved in generating the helical shape of Campylobacter. A C. jejuni transposon (Tn) mutant library was screened for non-helical mutants with inconsistent results...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27905873/comparative-genomics-of-beauveria-bassiana-uncovering-signatures-of-virulence-against-mosquitoes
#5
Claudio A Valero-Jiménez, Luigi Faino, Daphne Spring In't Veld, Sandra Smit, Bas J Zwaan, Jan A L van Kan
BACKGROUND: Entomopathogenic fungi such as Beauveria bassiana are promising biological agents for control of malaria mosquitoes. Indeed, infection with B. bassiana reduces the lifespan of mosquitoes in the laboratory and in the field. Natural isolates of B. bassiana show up to 10-fold differences in virulence between the most and the least virulent isolate. In this study, we sequenced the genomes of five isolates representing the extremes of low/high virulence and three RNA libraries, and applied a genome comparison approach to uncover genetic mechanisms underpinning virulence...
December 1, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27902881/the-chimeric-nature-of-the-genomes-of-marine-magnetotactic-coccoid-ovoid-bacteria-defines-a-novel-group-of-proteobacteria
#6
Boyang Ji, Sheng-Da Zhang, Wei-Jia Zhang, Zoe Rouy, François Alberto, Claire-Lise Santini, Sophie Mangenot, Séverine Gagnot, Nadège Philippe, Nathalie Pradel, Lichen Zhang, Sébastien Tempel, Ying Li, Claudine Médigue, Bernard Henrissat, Pedro M Coutinho, Valérie Barbe, Emmanuel Talla, Long-Fei Wu
Magnetotactic bacteria (MTB) are a group of phylogenetically and physiologically diverse Gram-negative bacteria that synthesize intracellular magnetic crystals named magnetosomes. MTB are affiliated with three classes of Proteobacteria phylum, Nitrospirae phylum, Omnitrophica phylum and probably with the candidate phylum Latescibacteria. The evolutionary origin and physiological diversity of MTB compared to other bacterial taxonomic groups remain to be illustrated. Here, we analyzed the genome of the marine magneto-ovoid strain MO-1 and found that it is closely related to Magnetococcus marinus MC-1...
November 30, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27902784/dynamic-in-vivo-mutations-within-the-ica-operon-during-persistence-of-staphylococcus-aureus-in-the-airways-of-cystic-fibrosis-patients
#7
Bianca Schwartbeck, Johannes Birtel, Janina Treffon, Lars Langhanki, Alexander Mellmann, Devika Kale, Janina Kahl, Nina Hirschhausen, Claudia Neumann, Jean C Lee, Friedrich Götz, Holger Rohde, Hanae Henke, Peter Küster, Georg Peters, Barbara C Kahl
Cystic fibrosis (CF) is associated with chronic bacterial airway infections leading to lung insufficiency and decreased life expectancy. Staphylococcus aureus is one of the most prevalent pathogens isolated from the airways of CF patients. Mucoid colony morphology has been described for Pseudomonas aeruginosa, the most common pathogen in CF, but not for S. aureus. From the airways of 8 of 313 CF patients (2.5%) mucoid S. aureus isolates (n = 115) were cultured with a mean persistence of 29 months (range 1 month, 126 months)...
November 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27902297/genome-analysis-based-reclassification-of-streptomyces-endus-and-streptomyces-sporocinereus-as-later-heterotypic-synonyms-of-streptomyces-hygroscopicus-subsp-hygroscopicus
#8
Hisayuki Komaki, Natsuko Ichikawa, Akio Oguchi, Moriyuki Hamada, Tomohiko Tamura, Nobuyuki Fujita, Ken-Ichiro Suzuki
The aim of this study is to reclarify the taxonomic relationship among Streptomyces hygroscopicus subsp. hygroscopicus, Streptomyces endus and Streptomyces sporocinereus. Whole genome shotgun sequencing was performed for the type strains of these three taxa. Average nucleotide identity and digital DNA-DNA hybridization values among the three taxa were greater than the thresholds for bacterial species delineation, indicating that they belong to the same genomospecies. In addition, their phenotypic data previously reported also support the synonymy...
October 28, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27902257/acinetobacter-larvae-sp-nov-isolated-from-the-larval-gut-of-omphisa-fuscidentalis
#9
Song Liu, Yanwei Wang, Zhiyong Ruan, Kedong Ma, Bo Wu, Yansheng Xu, Jingli Wang, Yang You, Mingxiong He, Guoquan Hu
A Gram-stain-negative, non-spore-forming, non-motile, and aerobic coccobacilli shaped strain, designated BRTC-1T, was isolated from the gut of Omphisa fuscidentalis Hampson, which is a larva of a moth and was collected from Xishuangbanna Dai Autonomous Prefecture in China. The isolate was found to grow at NaCl concentrations of 0-5 % (w/v) (optimum: 0 %), 10-45 ℃ (optimum: 30-35 ℃) and pH 5.0-9.0 (optimum: 6.0) on TSA. Analysis of the 16S rRNA gene sequence indicated that the isolate belongs to the genus Acinetobacter and most closely related to Acinetobacter rudis LMG 26107T, Acinetobacter guillouiae LMG 988T and Acinetobacter bereziniae LMG 1003T with 96...
November 8, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27893790/detection-of-a-cfr-b-variant-in-german-enterococcus-faecium-clinical-isolates-and-the-impact-on-linezolid-resistance-in-enterococcus-spp
#10
Jennifer K Bender, Carola Fleige, Ingo Klare, Stefan Fiedler, Alexander Mischnik, Nico T Mutters, Kate E Dingle, Guido Werner
The National Reference Centre for Staphylococci and Enterococci in Germany has received an increasing number of clinical linezolid-resistant E. faecium isolates in recent years. Five isolates harbored a cfr(B) variant gene locus the product of which is capable of conferring linezolid resistance. The cfr(B)-like methyltransferase gene was also detected in Clostridium difficile. Antimicrobial susceptibility was determined for cfr(B)-positive and linezolid-resistant E. faecium isolates and two isogenic C. difficile strains...
2016: PloS One
https://www.readbyqxmd.com/read/27890457/the-role-of-whole-genome-sequencing-wgs-in-antimicrobial-susceptibility-testing-of-bacteria-report-from-the-eucast-subcommittee
#11
REVIEW
Matthew J Ellington, Oskar Ekelund, Frank M Aarestrup, Rafael Canton, Michel Doumith, Christian Giske, Hajo Grundman, Henrik Hasman, Matthew Holden, Katie L Hopkins, Jon Iredell, Gunnar Kahlmeter, Claudio U Köser, Alasdair MacGowan, Dik Mevius, Mike Mulvey, Thierry Naas, Tim Peto, Jean-Marc Rolain, Ørjan Samuelsen, Neil Woodford
Whole genome sequencing (WGS) offers the potential to predict antimicrobial susceptibility from a single assay. The European Committee on Antimicrobial Susceptibility Testing (EUCAST) established a subcommittee to review the current development status of WGS for bacterial antimicrobial susceptibility testing (AST). The published evidence for using WGS as a tool to infer antimicrobial susceptibility accurately is currently either poor or non-existent and the evidence / knowledge base requires significant expansion...
November 23, 2016: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/27881417/analysis-of-germination-capacity-and-inventarisation-of-germinant-receptor-sub-clusters-of-genome-sequenced-bacillus-cereus-environmental-isolates-and-model-strains
#12
Alicja K Warda, Yinghua Xiao, Jos Boekhorst, Marjon H J Wells-Bennik, Masja N Nierop Groot, Tjakko Abee
: Spore germination of 17 Bacillus cereus food isolates and reference strains was evaluated using flow cytometry analysis in combination with fluorescent staining at a single spore level. This approach allowed for rapid collection of germination data in more than 20 conditions including heat activation of spores, germination in complex media (BHI and TSB), and exposure to saturating concentrations of single amino acids and the combination of alanine and inosine. Whole genome sequence comparison revealed a total of eleven clusters of operons encoded germinant receptors (GRs); GerK, GerI and GerL were present in all strains, whereas GerR, GerS, GerG, GerQ, GerX, GerF, GerW and GerZ (sub)clusters showed a more diverse presence/absence in different strains...
November 23, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27881098/genomic-determination-of-minimum-multi-locus-sequence-typing-schemas-to-represent-the-genomic-phylogeny-of-mycoplasma-hominis
#13
Aleksey Jironkin, Rebecca J Brown, Anthony Underwood, Victoria J Chalker, Owen B Spiller
BACKGROUND: Mycoplasma hominis is an opportunistic human pathogen, associated with clinically diverse disease. Currently, there is no standardised method for typing M. hominis, which would aid in understanding pathogen epidemiology and transmission. Due to availability and costs of whole genome sequencing and the challenges in obtaining adequate M. hominis DNA, the use of whole genome sequence analysis to provide clinical guidance is unpractical for this bacterial species as well as other fastidious organisms...
November 23, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27876778/differential-fecal-microbiota-are-retained-in-broiler-chicken-lines-divergently-selected-for-fatness-traits
#14
Qiangchuan Hou, Lai-Yu Kwok, Yi Zheng, Lifeng Wang, Zhuang Guo, Jiachao Zhang, Weiqiang Huang, Yuxiang Wang, Li Leng, Hui Li, Heping Zhang
Our study combined 16S rRNA-pyrosequencing and whole genome sequencing to analyze the fecal metagenomes of the divergently selected lean (LL) and fat (FL) line chickens. Significant structural differences existed in both the phylogenic and functional metagenomes between the two chicken lines. At phylum level, the FL group had significantly less Bacteroidetes. At genus level, fourteen genera of different relative abundance were identified, with some known short-chain fatty acid producers (including Subdoligranulum, Butyricicoccus, Eubacterium, Bacteroides, Blautia) and a potentially pathogenic genus (Enterococcus)...
November 23, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27871234/a-genome-wide-bac-end-sequence-survey-provides-first-insights-into-sweetpotato-ipomoea-batatas-l-lam-genome-composition
#15
Zengzhi Si, Bing Du, Jinxi Huo, Shaozhen He, Qingchang Liu, Hong Zhai
BACKGROUND: Sweetpotato, Ipomoea batatas (L.) Lam., is an important food crop widely grown in the world. However, little is known about the genome of this species because it is a highly heterozygous hexaploid. Gaining a more in-depth knowledge of sweetpotato genome is therefore necessary and imperative. In this study, the first bacterial artificial chromosome (BAC) library of sweetpotato was constructed. Clones from the BAC library were end-sequenced and analyzed to provide genome-wide information about this species...
November 21, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27870886/comparative-genomics-revealed-multiple-helicobacter-pylori-genes-associated-with-biofilm-formation-in-vitro
#16
Eric Hong Jian Wong, Chow Goon Ng, Eng Guan Chua, Alfred Chin Yen Tay, Fanny Peters, Barry J Marshall, Bow Ho, Khean Lee Goh, Jamuna Vadivelu, Mun Fai Loke
BACKGROUND: Biofilm formation by Helicobacter pylori may be one of the factors influencing eradication outcome. However, genetic differences between good and poor biofilm forming strains have not been studied. MATERIALS AND METHODS: Biofilm yield of 32 Helicobacter pylori strains (standard strain and 31 clinical strains) were determined by crystal-violet assay and grouped into poor, moderate and good biofilm forming groups. Whole genome sequencing of these 32 clinical strains was performed on the Illumina MiSeq platform...
2016: PloS One
https://www.readbyqxmd.com/read/27855063/in-vitro-tolerance-of-a-drug-na%C3%A3-ve-staphylococcus-aureus-fda209p-towards-vancomycin
#17
Madhuri Singh, Miki Matsuo, Takashi Sasaki, Yuh Morimoto, Tomomi Hishinuma, Keiichi Hiramatsu
The mechanisms underlying bacterial tolerance to antibiotics are unclear. A possible adaptation strategy has now been explored by exposure of drug-naïve methicillin-susceptible Staphylococcus aureus strain FDA209P to vancomycin in vitro Vancomycin-survivor strains, which appeared after 96 h of exposure, were slow-growing derivatives of the parent strain. Although the vancomycin minimum-inhibitory concentrations (MICs) with the survivor strains were within the susceptible range, the cytokilling effects of vancomycin at 20-fold MIC were significantly lower than those in the parent strain...
November 14, 2016: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/27854339/two-novel-myoviruses-from-the-north-of-iraq-reveal-insights-into-clostridium-difficile-phage-diversity-and-biology
#18
Srwa J Rashid, Jakub Barylski, Katherine R Hargreaves, Andrew A Millard, Gurinder K Vinner, Martha R J Clokie
Bacteriophages (phages) are increasingly being explored as therapeutic agents to combat bacterial diseases, including Clostridium difficile infections. Therapeutic phages need to be able to efficiently target and kill a wide range of clinically relevant strains. While many phage groups have yet to be investigated in detail, those with new and useful properties can potentially be identified when phages from newly studied geographies are characterised. Here, we report the isolation of C. difficile phages from soil samples from the north of Iraq...
November 16, 2016: Viruses
https://www.readbyqxmd.com/read/27852675/serotype-distribution-population-structure-and-antimicrobial-resistance-of-group-b-streptococcus-strains-recovered-from-colonized-pregnant-women
#19
Sarah Teatero, Patricia Ferrieri, Irene Martin, Walter Demczuk, Allison McGeer, Nahuel Fittipaldi
Using serotyping, multilocus sequence typing and whole-genome sequencing (WGS) of selected strains, we studied the population structure of 102 group B Streptococcus isolates prospectively sampled in 2014 from vaginal/rectal swabs of healthy pregnant women in metropolitan Toronto, Canada. We also determined the susceptibilities of all colonizing isolates to penicillin, erythromycin, clindamycin, tetracycline and other antimicrobial agents. Overall, we observed a high rate of tetracycline resistance (89%) among colonizing GBS...
November 16, 2016: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/27852235/enrichment-dynamics-of-listeria-monocytogenes-and-the-associated-microbiome-from-naturally-contaminated-ice-cream-linked-to-a-listeriosis-outbreak
#20
Andrea Ottesen, Padmini Ramachandran, Elizabeth Reed, James R White, Nur Hasan, Poorani Subramanian, Gina Ryan, Karen Jarvis, Christopher Grim, Ninalynn Daquiqan, Darcy Hanes, Marc Allard, Rita Colwell, Eric Brown, Yi Chen
BACKGROUND: Microbiota that co-enrich during efforts to recover pathogens from foodborne outbreaks interfere with efficient detection and recovery. Here, dynamics of co-enriching microbiota during recovery of Listeria monocytogenes from naturally contaminated ice cream samples linked to an outbreak are described for three different initial enrichment formulations used by the Food and Drug Administration (FDA), the International Organization of Standardization (ISO), and the United States Department of Agriculture (USDA)...
November 16, 2016: BMC Microbiology
keyword
keyword
104574
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"